Feature Papers: 'Plant Genetics and Genomics' Section

A topical collection in Genes (ISSN 2073-4425). This collection belongs to the section "Plant Genetics and Genomics".

Viewed by 37790

Editors

School of Biological Sciences, University of Nebraska, Lincoln 1901 Vine St., Lincoln, NE 68588-0660, USA
Interests: non-coding RNAs; miRNAs and siRNAs; epigenetics; functional genomics; plant molecular biology; genetics
Special Issues, Collections and Topics in MDPI journals
Department of Agricultural Sciences, University of Bologna, Viale Fanin 44, 40127 Bologna, Italy
Interests: Quantitative Trait Loci mapping; drought resistance; root system architecture; phenotyping; maize; durum wheat; barley
Special Issues, Collections and Topics in MDPI journals
School of Biological Sciences, The University of Western Australia, Crawley, WA 6009, Australia
Interests: crop genomics; brassica; disease resistance; pan genomics; evolutionary genomics; population genomics
Special Issues, Collections and Topics in MDPI journals

Topical Collection Information

Dear Colleagues,

This Topical Collection, “Feature Papers: ‘Plant Genetics and Genomics’ Section”, aims to collect high-quality research articles, review articles, and communications that cover key areas of plant genetics and genomics. Since the aim of this Topical Collection is to illustrate, through selected works, recent advances in the field of plant genetics and genomics, we encourage Editorial Board Members of the “Plant Genetics and Genomics” Section to contribute feature papers reflecting the latest progress in their research field, or to invite relevant experts and colleagues to make contributions to this Topical Collection. We aim to represent our Section as an attractive, open access publishing platform for plant genetics and genomics research.

Topics include, but are not limited to:

  • Chromatin remodelling and dynamics;
  • Epigenetics;
  • DNA replication, repair, recombination and mobile DNA;
  • Noncoding RNAs;
  • RNA modifications and editing;
  • Single-cell genomics;
  • Regulation of gene expression;
  • Plasmid and mitochondria genomic studies;
  • Mechanisms governing genetic phenomena, such as dominance, heterosis and self-incompatibility;
  • Plant genome editing;

Prof. Dr. Bin Yu
Prof. Dr. Roberto Tuberosa
Prof. Dr. Jacqueline Batley
Collection Editors

Manuscript Submission Information

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • plants
  • genetics
  • genomics
  • epigenetics
  • regulation of gene expression

Published Papers (16 papers)

2023

Jump to: 2022

20 pages, 3546 KiB  
Article
Seasonal Developing Xylem Transcriptome Analysis of Pinus densiflora Unveils Novel Insights for Compression Wood Formation
by Thi Thu Tram Nguyen, Min-Ha Kim, Eung-Jun Park, Hyoshin Lee and Jae-Heung Ko
Genes 2023, 14(9), 1698; https://doi.org/10.3390/genes14091698 - 26 Aug 2023
Viewed by 902
Abstract
Wood is the most important renewable resource not only for numerous practical utilizations but also for mitigating the global climate crisis by sequestering atmospheric carbon dioxide. The compressed wood (CW) of gymnosperms, such as conifers, plays a pivotal role in determining the structure [...] Read more.
Wood is the most important renewable resource not only for numerous practical utilizations but also for mitigating the global climate crisis by sequestering atmospheric carbon dioxide. The compressed wood (CW) of gymnosperms, such as conifers, plays a pivotal role in determining the structure of the tree through the reorientation of stems displaced by environmental forces and is characterized by a high content of lignin. Despite extensive studies on many genes involved in wood formation, the molecular mechanisms underlying seasonal and, particularly, CW formation remain unclear. This study examined the seasonal dynamics of two wood tissue types in Pinus densiflora: CW and opposite wood (OW). RNA sequencing of developing xylem for two consecutive years revealed comprehensive transcriptome changes and unique differences in CW and OW across seasons. During growth periods, such as spring and summer, we identified 2255 transcripts with differential expression in CW, with an upregulation in lignin biosynthesis genes and significant downregulation in stress response genes. Notably, among the laccases critical for monolignol polymerization, PdeLAC17 was found to be specifically expressed in CW, suggesting its vital role in CW formation. PdeERF4, an ERF transcription factor preferentially expressed in CW, seems to regulate PdeLAC17 activity. This research provides an initial insight into the transcriptional regulation of seasonal CW development in P. densiflora, forming a foundation for future studies to enhance our comprehension of wood formation in gymnosperms. Full article
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37 pages, 2571 KiB  
Review
Integrated Genomic Selection for Accelerating Breeding Programs of Climate-Smart Cereals
by Dwaipayan Sinha, Arun Kumar Maurya, Gholamreza Abdi, Muhammad Majeed, Rachna Agarwal, Rashmi Mukherjee, Sharmistha Ganguly, Robina Aziz, Manika Bhatia, Aqsa Majgaonkar, Sanchita Seal, Moumita Das, Swastika Banerjee, Shahana Chowdhury, Sherif Babatunde Adeyemi and Jen-Tsung Chen
Genes 2023, 14(7), 1484; https://doi.org/10.3390/genes14071484 - 21 Jul 2023
Cited by 7 | Viewed by 4911
Abstract
Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The rising population is posing increased demand for food, thereby pushing for an acceleration in agricultural production. Furthermore, increased anthropogenic activities have resulted in [...] Read more.
Rapidly rising population and climate changes are two critical issues that require immediate action to achieve sustainable development goals. The rising population is posing increased demand for food, thereby pushing for an acceleration in agricultural production. Furthermore, increased anthropogenic activities have resulted in environmental pollution such as water pollution and soil degradation as well as alterations in the composition and concentration of environmental gases. These changes are affecting not only biodiversity loss but also affecting the physio-biochemical processes of crop plants, resulting in a stress-induced decline in crop yield. To overcome such problems and ensure the supply of food material, consistent efforts are being made to develop strategies and techniques to increase crop yield and to enhance tolerance toward climate-induced stress. Plant breeding evolved after domestication and initially remained dependent on phenotype-based selection for crop improvement. But it has grown through cytological and biochemical methods, and the newer contemporary methods are based on DNA-marker-based strategies that help in the selection of agronomically useful traits. These are now supported by high-end molecular biology tools like PCR, high-throughput genotyping and phenotyping, data from crop morpho-physiology, statistical tools, bioinformatics, and machine learning. After establishing its worth in animal breeding, genomic selection (GS), an improved variant of marker-assisted selection (MAS), has made its way into crop-breeding programs as a powerful selection tool. To develop novel breeding programs as well as innovative marker-based models for genetic evaluation, GS makes use of molecular genetic markers. GS can amend complex traits like yield as well as shorten the breeding period, making it advantageous over pedigree breeding and marker-assisted selection (MAS). It reduces the time and resources that are required for plant breeding while allowing for an increased genetic gain of complex attributes. It has been taken to new heights by integrating innovative and advanced technologies such as speed breeding, machine learning, and environmental/weather data to further harness the GS potential, an approach known as integrated genomic selection (IGS). This review highlights the IGS strategies, procedures, integrated approaches, and associated emerging issues, with a special emphasis on cereal crops. In this domain, efforts have been taken to highlight the potential of this cutting-edge innovation to develop climate-smart crops that can endure abiotic stresses with the motive of keeping production and quality at par with the global food demand. Full article
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22 pages, 1482 KiB  
Review
Translation Arrest: A Key Player in Plant Antiviral Response
by Annemarie Vermeulen, Frank L. W. Takken and Victor A. Sánchez-Camargo
Genes 2023, 14(6), 1293; https://doi.org/10.3390/genes14061293 - 19 Jun 2023
Cited by 1 | Viewed by 1992
Abstract
Plants evolved several mechanisms to protect themselves against viruses. Besides recessive resistance, where compatible host factors required for viral proliferation are absent or incompatible, there are (at least) two types of inducible antiviral immunity: RNA silencing (RNAi) and immune responses mounted upon activation [...] Read more.
Plants evolved several mechanisms to protect themselves against viruses. Besides recessive resistance, where compatible host factors required for viral proliferation are absent or incompatible, there are (at least) two types of inducible antiviral immunity: RNA silencing (RNAi) and immune responses mounted upon activation of nucleotide-binding domain leucine-rich repeat (NLR) receptors. RNAi is associated with viral symptom recovery through translational repression and transcript degradation following recognition of viral double-stranded RNA produced during infection. NLR-mediated immunity is induced upon (in)direct recognition of a viral protein by an NLR receptor, triggering either a hypersensitive response (HR) or an extreme resistance response (ER). During ER, host cell death is not apparent, and it has been proposed that this resistance is mediated by a translational arrest (TA) of viral transcripts. Recent research indicates that translational repression plays a crucial role in plant antiviral resistance. This paper reviews current knowledge on viral translational repression during viral recovery and NLR-mediated immunity. Our findings are summarized in a model detailing the pathways and processes leading to translational arrest of plant viruses. This model can serve as a framework to formulate hypotheses on how TA halts viral replication, inspiring new leads for the development of antiviral resistance in crops. Full article
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20 pages, 2435 KiB  
Article
Integrative Transcriptomics Data Mining to Explore the Functions of TDP1α and TDP1β Genes in the Arabidopsis thaliana Model Plant
by Paola Pagano, Andrea Pagano, Stefano Paternolli, Alma Balestrazzi and Anca Macovei
Genes 2023, 14(4), 884; https://doi.org/10.3390/genes14040884 - 09 Apr 2023
Viewed by 1392
Abstract
The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3′-phosphate of DNA in the DNA–topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small TDP1 gene subfamily is present in plants, where TDP1α [...] Read more.
The tyrosyl-DNA phosphodiesterase 1 (TDP1) enzyme hydrolyzes the phosphodiester bond between a tyrosine residue and the 3′-phosphate of DNA in the DNA–topoisomerase I (TopI) complex, being involved in different DNA repair pathways. A small TDP1 gene subfamily is present in plants, where TDP1α has been linked to genome stability maintenance, while TDP1β has unknown functions. This work aimed to comparatively investigate the function of the TDP1 genes by taking advantage of the rich transcriptomics databases available for the Arabidopsis thaliana model plant. A data mining approach was carried out to collect information regarding gene expression in different tissues, genetic backgrounds, and stress conditions, using platforms where RNA-seq and microarray data are deposited. The gathered data allowed us to distinguish between common and divergent functions of the two genes. Namely, TDP1β seems to be involved in root development and associated with gibberellin and brassinosteroid phytohormones, whereas TDP1α is more responsive to light and abscisic acid. During stress conditions, both genes are highly responsive to biotic and abiotic treatments in a time- and stress-dependent manner. Data validation using gamma-ray treatments applied to Arabidopsis seedlings indicated the accumulation of DNA damage and extensive cell death associated with the observed changes in the TDP1 genes expression profiles. Full article
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22 pages, 1790 KiB  
Review
Machine Learning-Assisted Approaches in Modernized Plant Breeding Programs
by Mohsen Yoosefzadeh Najafabadi, Mohsen Hesami and Milad Eskandari
Genes 2023, 14(4), 777; https://doi.org/10.3390/genes14040777 - 23 Mar 2023
Cited by 18 | Viewed by 4779
Abstract
In the face of a growing global population, plant breeding is being used as a sustainable tool for increasing food security. A wide range of high-throughput omics technologies have been developed and used in plant breeding to accelerate crop improvement and develop new [...] Read more.
In the face of a growing global population, plant breeding is being used as a sustainable tool for increasing food security. A wide range of high-throughput omics technologies have been developed and used in plant breeding to accelerate crop improvement and develop new varieties with higher yield performance and greater resilience to climate changes, pests, and diseases. With the use of these new advanced technologies, large amounts of data have been generated on the genetic architecture of plants, which can be exploited for manipulating the key characteristics of plants that are important for crop improvement. Therefore, plant breeders have relied on high-performance computing, bioinformatics tools, and artificial intelligence (AI), such as machine-learning (ML) methods, to efficiently analyze this vast amount of complex data. The use of bigdata coupled with ML in plant breeding has the potential to revolutionize the field and increase food security. In this review, some of the challenges of this method along with some of the opportunities it can create will be discussed. In particular, we provide information about the basis of bigdata, AI, ML, and their related sub-groups. In addition, the bases and functions of some learning algorithms that are commonly used in plant breeding, three common data integration strategies for the better integration of different breeding datasets using appropriate learning algorithms, and future prospects for the application of novel algorithms in plant breeding will be discussed. The use of ML algorithms in plant breeding will equip breeders with efficient and effective tools to accelerate the development of new plant varieties and improve the efficiency of the breeding process, which are important for tackling some of the challenges facing agriculture in the era of climate change. Full article
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10 pages, 1963 KiB  
Article
RAD51 and RAD51B Play Diverse Roles in the Repair of DNA Double Strand Breaks in Physcomitrium patens
by Karel J. Angelis, Lenka Záveská Drábková, Radka Vágnerová and Marcela Holá
Genes 2023, 14(2), 305; https://doi.org/10.3390/genes14020305 - 24 Jan 2023
Cited by 4 | Viewed by 1423
Abstract
RAD51 is involved in finding and invading homologous DNA sequences for accurate homologous recombination (HR). Its paralogs have evolved to regulate and promote RAD51 functions. The efficient gene targeting and high HR rates are unique in plants only in the moss Physcomitrium patens [...] Read more.
RAD51 is involved in finding and invading homologous DNA sequences for accurate homologous recombination (HR). Its paralogs have evolved to regulate and promote RAD51 functions. The efficient gene targeting and high HR rates are unique in plants only in the moss Physcomitrium patens (P. patens). In addition to two functionally equivalent RAD51 genes (RAD1-1 and RAD51-2), other RAD51 paralogues were also identified in P. patens. For elucidation of RAD51’s involvement during DSB repair, two knockout lines were constructed, one mutated in both RAD51 genes (Pprad51-1-2) and the second with mutated RAD51B gene (Pprad51B). Both lines are equally hypersensitive to bleomycin, in contrast to their very different DSB repair efficiency. Whereas DSB repair in Pprad51-1-2 is even faster than in WT, in Pprad51B, it is slow, particularly during the second phase of repair kinetic. We interpret these results as PpRAD51-1 and -2 being true functional homologs of ancestral RAD51 involved in the homology search during HR. Absence of RAD51 redirects DSB repair to the fast NHEJ pathway and leads to a reduced 5S and 18S rDNA copy number. The exact role of the RAD51B paralog remains unclear, though it is important in damage recognition and orchestrating HR response. Full article
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2022

Jump to: 2023

17 pages, 3897 KiB  
Article
Orchid NAC Transcription Factors: A Focused Analysis of CUPULIFORMIS Genes
by Maria Carmen Valoroso, Francesca Lucibelli and Serena Aceto
Genes 2022, 13(12), 2293; https://doi.org/10.3390/genes13122293 - 05 Dec 2022
Cited by 2 | Viewed by 1419
Abstract
Plant transcription factors are involved in different developmental pathways. NAC transcription factors (No Apical Meristem, Arabidopsis thaliana Activating Factor, Cup-shaped Cotyledon) act in various processes, e.g., plant organ formation, response to stress, and defense mechanisms. In Antirrhinum majus, the NAC transcription factor CUPULIFORMIS [...] Read more.
Plant transcription factors are involved in different developmental pathways. NAC transcription factors (No Apical Meristem, Arabidopsis thaliana Activating Factor, Cup-shaped Cotyledon) act in various processes, e.g., plant organ formation, response to stress, and defense mechanisms. In Antirrhinum majus, the NAC transcription factor CUPULIFORMIS (CUP) plays a role in determining organ boundaries and lip formation, and the CUP homologs of Arabidopsis and Petunia are involved in flower organ formation. Orchidaceae is one of the most species-rich families of angiosperms, known for its extraordinary diversification of flower morphology. We conducted a transcriptome and genome-wide analysis of orchid NACs, focusing on the No Apical Meristem (NAM) subfamily and CUP genes. To check whether the CUP homologs could be involved in the perianth formation of orchids, we performed an expression analysis on the flower organs of the orchid Phalaenopsis aphrodite at different developmental stages. The expression patterns of the CUP genes of P. aphrodite suggest their possible role in flower development and symmetry establishment. In addition, as observed in other species, the orchid CUP1 and CUP2 genes seem to be regulated by the microRNA, miR164. Our results represent a preliminary study of NAC transcription factors in orchids to understand the role of these genes during orchid flower formation. Full article
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10 pages, 5128 KiB  
Article
PhMYB37 Promotes Shoot Branching in Petunia
by Lili Dong, Tianyin Yang, Di Gao, Tian Wang and Xinyi Deng
Genes 2022, 13(11), 2064; https://doi.org/10.3390/genes13112064 - 08 Nov 2022
Cited by 1 | Viewed by 1051
Abstract
Petunia is one of the world’s most important flowers, and its branch development has long been a source of discussion. MYB transcription factors have been identified as important plant branching regulators. In this study, 113 R2R3-MYB genes were identified from the petunia genome. [...] Read more.
Petunia is one of the world’s most important flowers, and its branch development has long been a source of discussion. MYB transcription factors have been identified as important plant branching regulators. In this study, 113 R2R3-MYB genes were identified from the petunia genome. PhMYB genes, closely related to RAXs, were expressed at greater levels in axillary buds and roots. Decapitation and 6-BA did not regulate the expression of PhMYB37. PhMYB37 was localized in the nucleus. Heterologous overexpression of PhMYB37 promoted shoot branching in transgenic Arabidopsis while silencing of PhMYB37 inhibited shoot branching. These results suggest that PhMYB37 plays a critical and positive role in petunia shoot branching. Full article
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25 pages, 3741 KiB  
Article
Simple Sequence Repeat Markers Reveal Genetic Diversity and Population Structure of Bolivian Wild and Cultivated Tomatoes (Solanum lycopersicum L.)
by Evelyn E. Villanueva-Gutierrez, Eva Johansson, Maria Luisa Prieto-Linde, Alberto Centellas Quezada, Marie E. Olsson and Mulatu Geleta
Genes 2022, 13(9), 1505; https://doi.org/10.3390/genes13091505 - 23 Aug 2022
Cited by 2 | Viewed by 1902
Abstract
The western part of South America is a centre of diversity for tomatoes, but genetic diversity studies are lacking for parts of that region, including Bolivia. We used 11 simple sequence repeat (SSR) markers (including seven novel markers) to evaluate genetic diversity and [...] Read more.
The western part of South America is a centre of diversity for tomatoes, but genetic diversity studies are lacking for parts of that region, including Bolivia. We used 11 simple sequence repeat (SSR) markers (including seven novel markers) to evaluate genetic diversity and population structure of 28 accessions (four modern cultivars, four advanced lines, nine landraces, 11 wild populations), and to compare their genetic variation against phenotypic traits, geographical origin and altitude. In total, 33 alleles were detected across all loci, with 2–5 alleles per locus. The top three informative SSRs were SLM6-11, LE20592 and TomSatX11-1, with polymorphism information content (PIC) of 0.65, 0.55 and 0.49, respectively. The genetic diversity of Bolivian tomatoes was low, as shown by mean expected heterozygosity (He) of 0.07. Analysis of molecular variance (AMOVA) revealed that 77.3% of the total variation was due to variation between accessions. Significant genetic differentiation was found for geographical origin, cultivation status, fruit shape, fruit size and growth type, each explaining 16–23% of the total variation. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) tree and principal coordinate analysis (PCoA) scatter plot both revealed differentiation between accessions with determinate flowers and accessions with indeterminate flowers, regardless of cultivation status. The genetic profiles of the accessions suggest that the Bolivian tomato gene pool comprises both strictly self-pollinating and open-pollinating genotypes. Full article
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30 pages, 5519 KiB  
Article
Zebularine, a DNA Methylation Inhibitor, Activates Anthocyanin Accumulation in Grapevine Cells
by Junhua Kong, Virginie Garcia, Enric Zehraoui, Linda Stammitti, Ghislaine Hilbert, Christel Renaud, Stéphane Maury, Alain Delaunay, Stéphanie Cluzet, Fatma Lecourieux, David Lecourieux, Emeline Teyssier and Philippe Gallusci
Genes 2022, 13(7), 1256; https://doi.org/10.3390/genes13071256 - 15 Jul 2022
Cited by 4 | Viewed by 2002
Abstract
Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. [...] Read more.
Through its role in the regulation of gene expression, DNA methylation can participate in the control of specialized metabolite production. We have investigated the link between DNA methylation and anthocyanin accumulation in grapevine using the hypomethylating drug, zebularine and Gamay Teinturier cell suspensions. In this model, zebularine increased anthocyanin accumulation in the light, and induced its production in the dark. To unravel the underlying mechanisms, cell transcriptome, metabolic content, and DNA methylation were analyzed. The up-regulation of stress-related genes, as well as a decrease in cell viability, revealed that zebularine affected cell integrity. Concomitantly, the global DNA methylation level was only slightly decreased in the light and not modified in the dark. However, locus-specific analyses demonstrated a decrease in DNA methylation at a few selected loci, including a CACTA DNA transposon and a small region upstream from the UFGT gene, coding for the UDP glucose:flavonoid-3-O-glucosyltransferase, known to be critical for anthocyanin biosynthesis. Moreover, this decrease was correlated with an increase in UFGT expression and in anthocyanin content. In conclusion, our data suggest that UFGT expression could be regulated through DNA methylation in Gamay Teinturier, although the functional link between changes in DNA methylation and UFGT transcription still needs to be demonstrated. Full article
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13 pages, 1094 KiB  
Review
Current Understanding of the Genetics and Molecular Mechanisms Regulating Wood Formation in Plants
by Min-Ha Kim, Eun-Kyung Bae, Hyoshin Lee and Jae-Heung Ko
Genes 2022, 13(7), 1181; https://doi.org/10.3390/genes13071181 - 30 Jun 2022
Cited by 8 | Viewed by 2800
Abstract
Unlike herbaceous plants, woody plants undergo volumetric growth (a.k.a. secondary growth) through wood formation, during which the secondary xylem (i.e., wood) differentiates from the vascular cambium. Wood is the most abundant biomass on Earth and, by absorbing atmospheric carbon dioxide, functions as one [...] Read more.
Unlike herbaceous plants, woody plants undergo volumetric growth (a.k.a. secondary growth) through wood formation, during which the secondary xylem (i.e., wood) differentiates from the vascular cambium. Wood is the most abundant biomass on Earth and, by absorbing atmospheric carbon dioxide, functions as one of the largest carbon sinks. As a sustainable and eco-friendly energy source, lignocellulosic biomass can help address environmental pollution and the global climate crisis. Studies of Arabidopsis and poplar as model plants using various emerging research tools show that the formation and proliferation of the vascular cambium and the differentiation of xylem cells require the modulation of multiple signals, including plant hormones, transcription factors, and signaling peptides. In this review, we summarize the latest knowledge on the molecular mechanism of wood formation, one of the most important biological processes on Earth. Full article
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25 pages, 3144 KiB  
Article
Mapping-by-Sequencing Reveals Genomic Regions Associated with Seed Quality Parameters in Brassica napus
by Hanna Marie Schilbert, Boas Pucker, David Ries, Prisca Viehöver, Zeljko Micic, Felix Dreyer, Katrin Beckmann, Benjamin Wittkop, Bernd Weisshaar and Daniela Holtgräwe
Genes 2022, 13(7), 1131; https://doi.org/10.3390/genes13071131 - 23 Jun 2022
Cited by 4 | Viewed by 3522
Abstract
Rapeseed (Brassica napus L.) is an important oil crop and has the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has high nutritional value for humans. Seed protein content (SPC) and [...] Read more.
Rapeseed (Brassica napus L.) is an important oil crop and has the potential to serve as a highly productive source of protein. This protein exhibits an excellent amino acid composition and has high nutritional value for humans. Seed protein content (SPC) and seed oil content (SOC) are two complex quantitative and polygenic traits which are negatively correlated and assumed to be controlled by additive and epistatic effects. A reduction in seed glucosinolate (GSL) content is desired as GSLs cause a stringent and bitter taste. The goal here was the identification of genomic intervals relevant for seed GSL content and SPC/SOC. Mapping by sequencing (MBS) revealed 30 and 15 new and known genomic intervals associated with seed GSL content and SPC/SOC, respectively. Within these intervals, we identified known but also so far unknown putatively causal genes and sequence variants. A 4 bp insertion in the MYB28 homolog on C09 shows a significant association with a reduction in seed GSL content. This study provides insights into the genetic architecture and potential mechanisms underlying seed quality traits, which will enhance future breeding approaches in B. napus. Full article
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15 pages, 3203 KiB  
Article
A Single Amino Acid Substitution in RFC4 Leads to Endoduplication and Compromised Resistance to DNA Damage in Arabidopsis thaliana
by Kan Cui, Lei Qin, Xianyu Tang, Jieying Nong, Jin Chen, Nan Wu, Xin Gong, Lixiong Yi, Chenghuizi Yang and Shitou Xia
Genes 2022, 13(6), 1037; https://doi.org/10.3390/genes13061037 - 09 Jun 2022
Cited by 1 | Viewed by 1645
Abstract
Replication factor C (RFC) is a heteropentameric ATPase associated with the diverse cellular activities (AAA+ATPase) protein complex, which is composed of one large subunit, known as RFC1, and four small subunits, RFC2/3/4/5. Among them, RFC1 and RFC3 were previously reported to mediate genomic [...] Read more.
Replication factor C (RFC) is a heteropentameric ATPase associated with the diverse cellular activities (AAA+ATPase) protein complex, which is composed of one large subunit, known as RFC1, and four small subunits, RFC2/3/4/5. Among them, RFC1 and RFC3 were previously reported to mediate genomic stability and resistance to pathogens in Arabidopsis. Here, we generated a viable rfc4e (rfc4−1/RFC4G54E) mutant with a single amino acid substitution by site-directed mutagenesis. Three of six positive T2 mutants with the same amino acid substitution, but different insertion loci, were sequenced to identify homozygotes, and the three homozygote mutants showed dwarfism, early flowering, and a partially sterile phenotype. RNA sequencing revealed that genes related to DNA repair and replication were highly upregulated. Moreover, the frequency of DNA lesions was found to be increased in rfc4e mutants. Consistent with this, the rfc4e mutants were very sensitive to DSB-inducing genotoxic agents. In addition, the G54E amino acid substitution in AtRFC4 delayed cell cycle progression and led to endoduplication. Overall, our study provides evidence supporting the notion that RFC4 plays an important role in resistance to genotoxicity and cell proliferation by regulating DNA damage repair in Arabidopsis thaliana. Full article
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13 pages, 4156 KiB  
Article
Genome-Wide Analysis and Exploration of WRKY Transcription Factor Family Involved in the Regulation of Shoot Branching in Petunia
by Huanyu Yao, Tianyin Yang, Jie Qian, Xinyi Deng and Lili Dong
Genes 2022, 13(5), 855; https://doi.org/10.3390/genes13050855 - 11 May 2022
Cited by 6 | Viewed by 1667
Abstract
The WRKY transcription factors (TFs) participate in various physiological, growth and developmental processes of plants. In our study, a total of 79 WRKY family members were identified and classified into three groups (Group I, Group IIa–e, and Group III) based on phylogenetic and [...] Read more.
The WRKY transcription factors (TFs) participate in various physiological, growth and developmental processes of plants. In our study, a total of 79 WRKY family members were identified and classified into three groups (Group I, Group IIa–e, and Group III) based on phylogenetic and conservative domain analyses. Conserved motif analysis showed that seven WRKYGQK domains changed. The promoter sequence analysis suggested that there were multiple stress- and hormone-related cis-regulatory elements in the promoter regions of PhWRKY genes. Expression patterns of PhWRKYs based on RNA-seq data revealed their diverse expression profiles in five tissues and under different treatments. Subcellular localization analysis showed that PhWRKY71 was located in the nucleus. In addition, overexpression of PhWRKY71 caused a significant increase in branch number. This indicated that PhWRKY71 played a critical role in regulating the shoot branching of Petuniahybrida. The above results lay the foundation for further revealing the functions of PhWRKY genes. Full article
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16 pages, 3770 KiB  
Article
Genome-Wide Identification of YABBY Gene Family in Cucurbitaceae and Expression Analysis in Cucumber (Cucumis sativus L.)
by Shuai Yin, Sen Li, Yiming Gao, Ezra S. Bartholomew, Ruijia Wang, Hua Yang, Chang Liu, Xiaofeng Chen, Ying Wang, Xingwang Liu and Huazhong Ren
Genes 2022, 13(3), 467; https://doi.org/10.3390/genes13030467 - 07 Mar 2022
Cited by 10 | Viewed by 3007
Abstract
YABBY transcription factors play important roles in plant growth and development. However, little is known about YABBY genes in Cucurbitaceae. Here, we identified 59 YABBY genes from eight cucurbit species, including cucumber (C. sativus L.), melon (C. melon L.), watermelon [...] Read more.
YABBY transcription factors play important roles in plant growth and development. However, little is known about YABBY genes in Cucurbitaceae. Here, we identified 59 YABBY genes from eight cucurbit species, including cucumber (C. sativus L.), melon (C. melon L.), watermelon (C. lanatus), wax gourd (B. hispida), pumpkin (C. maxima), zucchini (C. pepo L.), silver-seed gourd (C. argyrosperma), and bottle gourd (L. siceraria). The 59 YABBY genes were clustered into five subfamilies wherein the gene structures and motifs are conserved, suggesting similar functions within each subfamily. Different YABBY gene numbers in eight cucurbit species indicated that gene loss or duplication events exist in an evolutionary process across Cucurbitaceae. The cis-acting elements analysis implied that the YABBYs may be involved in plant development, and phytohormone, stress, and light responses. Importantly, YABBY genes exhibited organ-specific patterns in expression in cucumber. Furthermore, a gene CsaV3_6G038650 was constitutively expressed at higher levels at different fruit development stages and might play a crucial role in cucumber fruit development. Collectively, our work will provide a better understanding for further function identifications of YABBY genes in Cucurbitaceae. Full article
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19 pages, 3113 KiB  
Article
Combining Fine Mapping, Whole-Genome Re-Sequencing, and RNA-Seq Unravels Candidate Genes for a Soybean Mutant with Short Petioles and Weakened Pulvini
by Keke Kong, Mengge Xu, Zhiyong Xu, Ripa Akter Sharmin, Mengchen Zhang and Tuanjie Zhao
Genes 2022, 13(2), 185; https://doi.org/10.3390/genes13020185 - 21 Jan 2022
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Abstract
A short petiole is an important agronomic trait for the development of plant ideotypes with high yields. However, the genetic basis underlying this trait remains unclear. Here, we identified and characterized a novel soybean mutant with short petioles and weakened pulvini, designated as [...] Read more.
A short petiole is an important agronomic trait for the development of plant ideotypes with high yields. However, the genetic basis underlying this trait remains unclear. Here, we identified and characterized a novel soybean mutant with short petioles and weakened pulvini, designated as short petioles and weakened pulvini (spwp). Compared with the wild type (WT), the spwp mutant displayed shortened petioles, owing to the longitudinally decreased cell length, and exhibited a smaller pulvinus structure due to a reduction in motor cell proliferation and expansion. Genetic analysis showed that the phenotype of the spwp mutant was controlled by two recessive nuclear genes, named as spwp1 and spwp2. Using a map-based cloning strategy, the spwp1 locus was mapped in a 183 kb genomic region on chromosome 14 between markers S1413 and S1418, containing 15 annotated genes, whereas the spwp2 locus was mapped in a 195 kb genomic region on chromosome 11 between markers S1373 and S1385, containing 18 annotated genes. Based on the whole-genome re-sequencing and RNA-seq data, we identified two homologous genes, Glyma.11g230300 and Glyma.11g230600, as the most promising candidate genes for the spwp2 locus. In addition, the RNA-seq analysis revealed that the expression levels of genes involved in the cytokinin and auxin signaling transduction networks were altered in the spwp mutant compared with the WT. Our findings provide new gene resources for insights into the genetic mechanisms of petiole development and pulvinus establishment, as well as soybean ideotype breeding. Full article
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